"While Iran has obligations, it also has rights. The agency should preserve its credibility," charged Iranian Foreign Ministry spokesman Nasser Kanaani.
North Korea has conducted six nuclear tests since 2006. It has also tested ballistic missiles capable of reaching the United States.
The IAEA announcement came a day after it said the same thing had happened at the radioactive waste facilities at Chernobyl, near the defunct power plant.
Serbia is one of the few European countries publicly pursuing stronger ties with Tehran.
On Thursday, the IAEA said that Tehran was already deep into preparations to make its threats a reality.
"The Zionists want to take revenge because of our progress in the way to lift sanctions... We will not fall into their trap...We will not allow this act of sabotage to affect the nuclear talks."
While the amount of enriched uranium extracted is small, it amounts to a fresh breach at a delicate stage, as the US and Iran hold indirect talks in Vienna regarding a renegotiation of the deal.
"Things are moving in the right direction, and we have had positive signals this week and especially in the last few days," a French diplomatic source said.
In the past year, North Korea displayed new short-range, medium-range, submarine-launched and intercontinental ballistic missile systems at military parades, the UN report said.
The move is the latest of several recent announcements by Iran to the International Atomic Energy Agency that it plans to further breach the nuclear deal.